4.1.0

Added

• Added a BAM/CRAM conversion to FASTQ step to run tools that depend on FASTQ files. It still is advised to supply a FASTQ file if possible to reduce runtime of the pipeline. #783

Fixed

• Fix issue with vcf_collect when no fusions are found by fusioninspector #786

3.0.1b

Patch fix for vcf_collect.py in cases when FusionInspector is empty but staying compatible with references from 3.0.1

4.0.0

Major changes include

• Recommended download of reference with aws --no-sign-request s3 sync s3://nf-core-awsmegatests/rnafusion/references/ <path_to_references>
• Changed reference fasta file to the primary assembly, moved from ensembl 102 to gencode 46
• New option to avoid using COSMIC --no_cosmic
• New option to skip generating the VCF summary: --skip_vcf
• New tool: CTAT-Splicing to detect cancer splicing events
• Introduced support to start from CRAM/BAM files and (splice) junctions files
• Fusion-report score is now called the fusion indication index (FII)
• Extra trimming for FusionCatcher in case reads are larger than 100 bp
• Single alignment for arriba and STAR-Fusion
• Use of a parameter --tools STRING to select which tools to enable

3.0.2

Bug fixes.

Changelog:

Changed

• Update to nf-tools 2.11.1 [https://github.com//pull/457] (#457)
• Update picard collectrnaseqmetrics memory requirements to 0.8x what is provided #474

Fixed

• fix bug when using parameter "whitelist" #466
• fix VCF_COLLECT handling when a tool is absent from FUSIONREPORT report #458
• fix VCF_COLLECT when fusioninspector output is empty but fusionreport is not #465
• fix VCF_COLLECT bug #481
• fix conda package for starfusion/detecthttps://github.com//pull/482
• fix logical gate so when stringtie should run but not starfusion, starfusion will not runhttps://github.com//pull/482

3.0.1

Patch to fix software versions output

3.0.0

Main changes:

• Squid and pizzly are no longuer supported
• Removed --fusioninspector_filter and --fusionreport_filter in favor of --tools_cutoff (default = 1, no filters applied)
• Removed FusionGDB from fusion-report
• Improved vcf file creation, using --annotate --examine_coding_effect with fusioninspector to collect more data
• Removed harsh trimming option, fastp trimming still available
• Removed qualimap rna_seq

Bug fixes:

• building references is possible without a samplesheet
• Fix channel i/o issue in StringTie workflow
• Various fusion-report issues with download
• Improved CI

2.4.0

Changelog:

Changed

• Use institutional configs by default #381
• Remove redundant indexing in starfusion and qc workflows #387
• Output bai files in same directory as bam files #387
• Update and review documentation #396
• Update picard container for PICARD_COLLECTRNASEQMETRICS to 3.0.0 #395
• Renamed output files #395
  • Arriba visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation
  • cram file from output bam of STAR_FOR_ARRIBA: meta.id to meta.id_star_for_arriba
  • cram file from output bam of STAR_FOR_STARFUSION: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out
  • fusion-report index.html file to meta.id_fusionreport_index.html
  • meta.id.vcf output from MEGAFUSION to meta.id_fusion_data.vcf

Fixed

• Tail trimming for reverse reads #379
• Set html files as optional in fusionreport #380
• Provide gene count file by default when running STAR_FOR_STARFUSION #385
• Fix fusion-report issue with MACOXS directories #386
• The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation #388
• Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases #403

Removed

• samtools sort and samtools index for arriba workflow were dispensable and were removed #395
• Removed trimmed fastqc report from multiqc #394

New Contributors

• @fevac made their first contribution in #379
• @efgstone made their first contribution in #382

Full Changelog: 2.3.4...2.4.0

2.3.4

Fix for megafusion

2.3.3

Fix for megafusion (again)

2.3.2

Fixes for megafusion